I've been playing since open world was open in Alpha, and I know how the boarding works, I captured plenty of ships before EA. But, since EA was released I've found that on 5 occasions a ship I board completely sinks immediately after Boarding Won. The ship is then not available to Capture or shown in the after battle report. Am I doing something wrong?

XP should be fairly low, maybe 1/4 of what you get from Combat Missions. But Gold should be higher in reward. Say you get 2k for Combat Missions, you should get 4k for Trade Missions. You can also increase the reward with distance traveled, which should also increase the likelihood of combat or attack.

There should be no exploration experience. If it were to be implemented, it should be menial. 5-10 XP per port. The real reason for exploring, is for gaining knowledge of the Production and Consumption of ports. Which then allows you to find the best prices for buying and selling goods, which makes you more money.

You don't need to travel long distances to trade. You just need to find a port which produces a good at a high rate, and then sell that good at a port that consumes that good at a high rate. So you're buying low, and selling high. It could be across the map, it could be across the island.

Well, in all reality, sinking any ship of an opposing faction, or capturing it, helps your nation. The enemy lost durability of a ship, they lose their hold items. Thus, very slightly making their nation less powerful in regards to attack and defense of their assets. All the while, you gain experience for larger ships, gold, xp, and their hold. So, you and your nation have gained, they and their nation have lost.
That's how I think of it at least.

I always had thought something that allowed you to look out from the port, towards the harbor would be good. This way you could see what all was happening, if an enemy fleet was approaching, if a ship was passing, if someone new came to port, etc. As well as being able to see the time of day and the weather. Rough mockup:

It's also important to note, that the primary benefit of exploration is the ability to learn the 'supply and demand' of a port. So that you know which ports produce product X at a reduced rate, and which ports consume product X at a high rate, so that your sale nets you a decent return. You'll end up finding yourself forced away from specific locales when another nation comes to rip the ports out of your hands.

It prevents the hoarding of ships. Forcing you to break them down for crafting, sell them, or put them on the market, etc. I see no issue with limiting the number of ships to 5 in ports. Perhaps there could be a feature similar to 'Expand Warehouse' where you buy more harbor space for your ships.